Contacts of the helix formed by residues 106 - 117 (chain M) in PDB entry 6CM9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 106 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95M PHE* 3.3 45.2 - - + +
102M SER* 3.1 25.4 + - - +
103M ILE 3.9 0.2 + - - -
104M ARG 3.7 0.2 - - - -
105M ASP* 1.3 88.3 - - - +
107M PHE* 1.3 55.2 + - - +
108M VAL* 3.1 8.6 - - - +
109M ILE* 3.0 11.7 + - + +
110M ILE* 2.8 31.2 + - + +
137M GLN* 4.0 14.3 + - - +
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Residues in contact with PHE 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 3.6 29.2 - - + -
38B ILE* 3.6 27.9 - - + +
39B ALA* 3.6 21.8 - - + -
42B THR* 4.3 11.7 - - + +
68B LEU* 5.7 0.5 - - - +
17M ILE* 5.0 2.7 - - + -
103M ILE 3.8 10.5 + - - +
104M ARG* 3.9 22.4 - - - -
105M ASP 4.4 7.4 - - - -
106M ASN* 1.3 75.6 - - - +
108M VAL* 1.3 78.3 + - + +
110M ILE* 4.1 6.7 - - - +
111M TYR* 3.2 40.6 + - + +
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Residues in contact with VAL 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 3.6 39.3 - - + +
38B ILE* 5.4 0.7 - - - -
64B GLU* 4.2 16.8 - - + +
68B LEU* 4.5 9.3 - - + +
105M ASP 5.4 3.6 - - - +
106M ASN* 4.8 2.9 - - - +
107M PHE* 1.3 99.2 - - + +
109M ILE* 1.3 60.5 + - + +
111M TYR* 5.3 0.3 - - - +
112M GLU* 3.1 35.4 + - - +
136M THR 6.1 0.7 - - - +
137M GLN* 6.3 2.7 - - - -
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Residues in contact with ILE 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94M TYR* 3.8 27.6 - - + -
95M PHE* 3.6 26.2 - - + -
106M ASN* 3.0 21.2 + - + +
108M VAL* 1.3 82.8 - - + +
110M ILE* 1.3 60.8 + - - +
111M TYR 3.4 2.0 - - - -
112M GLU* 3.2 7.9 + - - +
113M LEU* 2.8 26.7 + - + +
135M ILE* 3.8 17.9 - - + -
136M THR 3.5 10.3 - - - +
137M GLN* 3.4 42.2 - - + +
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Residues in contact with ILE 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ILE* 3.7 29.6 - - + -
91M PHE* 3.7 26.5 - - + -
95M PHE* 3.6 35.9 - - + -
102M SER 3.7 3.6 - - - +
103M ILE* 3.7 39.5 - - + +
106M ASN 2.8 21.5 + - - +
108M VAL 3.8 0.2 - - - -
109M ILE* 1.3 73.2 - - - +
111M TYR* 1.3 61.7 + - - +
113M LEU* 3.2 5.4 + - + +
114M LEU* 2.9 32.1 + - + +
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Residues in contact with TYR 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.1 10.9 + - + -
41B MET* 4.4 12.6 + - + +
42B THR* 2.7 42.6 + - - -
68B LEU* 6.3 2.0 - - + -
71B LEU* 3.5 44.4 - - + +
75B ASN* 5.3 1.3 - - - -
17M ILE* 3.5 27.4 - - + +
18M CYS* 3.5 30.1 + - - -
19M ARG* 4.2 11.6 + - + -
107M PHE* 3.2 29.1 + - + +
108M VAL 5.3 0.2 - - - +
109M ILE 3.4 0.4 - - - -
110M ILE* 1.3 77.2 - - - +
112M GLU* 1.3 59.7 + - + +
114M LEU* 3.8 3.2 - - + +
115M ASP* 2.9 28.6 + - - +
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Residues in contact with GLU 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 3.7 28.7 - - - +
67B LYS* 3.5 37.9 - - + +
68B LEU* 4.0 7.1 - - + +
108M VAL* 3.1 24.8 - - - +
109M ILE* 3.2 13.0 + - - +
111M TYR* 1.3 77.0 - - + +
113M LEU* 1.3 59.6 + - - +
115M ASP* 3.3 9.8 + - - +
116M GLU* 2.9 29.1 + - - +
135M ILE* 4.3 28.3 - - + +
136M THR 4.7 6.8 + - - +
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Residues in contact with LEU 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90M VAL* 4.2 6.7 - - + -
91M PHE* 3.6 34.8 - - + -
94M TYR* 3.6 42.6 - - + -
95M PHE* 4.9 3.4 - - + -
109M ILE* 2.8 21.8 + - + +
110M ILE* 3.2 8.2 + - - +
112M GLU* 1.3 77.0 - - - +
114M LEU* 1.3 58.3 + - - +
116M GLU* 2.9 3.5 + - + +
117M LEU* 2.8 39.4 + - + +
131M LEU* 3.9 24.2 - - + -
135M ILE* 3.7 17.0 - - + -
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Residues in contact with LEU 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M VAL* 4.2 27.6 - - + +
8M VAL* 5.4 3.4 - - + -
17M ILE* 4.6 16.6 - - + -
19M ARG* 3.7 30.7 - - + +
21M TYR* 2.6 45.3 + - - +
83M PHE* 5.1 2.0 - - + -
87M VAL* 4.7 7.9 - - + -
91M PHE* 4.5 15.5 - - + -
110M ILE* 2.9 30.7 + - + +
111M TYR* 4.3 2.5 - - - +
113M LEU* 1.3 74.7 - - - +
115M ASP* 1.3 59.2 + - - +
117M LEU* 4.3 18.8 - - + +
118M MET 3.7 2.1 + - - +
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Residues in contact with ASP 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 5.4 10.5 + - + +
74B MET* 4.5 6.2 - - - +
105B LEU* 3.4 27.7 - - - +
108B ARG* 3.5 25.4 + - - +
109B THR* 5.5 0.2 + - - -
19M ARG* 2.6 30.9 + - - +
111M TYR 2.9 19.7 + - - +
112M GLU* 3.3 10.8 - - - +
113M LEU 3.1 0.2 - - - -
114M LEU* 1.3 78.5 - - - +
116M GLU* 1.3 60.5 + - - +
118M MET 3.6 1.6 - - - +
119M ASP* 3.4 20.3 - - - +
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Residues in contact with GLU 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 5.8 1.0 + - - -
101B LEU* 4.8 2.4 - - - +
108B ARG* 3.7 10.4 + - - -
136B TYR* 2.7 31.7 + - - -
112M GLU 2.9 15.2 + - - +
113M LEU* 2.9 7.6 + - - +
115M ASP* 1.3 78.7 - - - +
117M LEU* 1.3 66.1 + - + +
118M MET 3.4 0.6 + - - -
124M GLN* 3.7 18.7 + - - +
125M THR* 4.0 10.9 + - - +
131M LEU* 3.7 21.1 - - + -
134M TYR* 2.6 39.6 + - + +
135M ILE* 4.5 9.9 - - + +
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Residues in contact with LEU 117 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M PHE* 4.0 13.2 - - + -
87M VAL* 3.8 31.6 - - + -
90M VAL* 4.2 19.5 - - + -
91M PHE* 5.2 1.8 - - + -
113M LEU* 2.8 29.4 + - + +
114M LEU* 4.3 12.6 - - + -
116M GLU* 1.3 73.7 - - + +
118M MET* 1.3 59.7 + - + +
123M PRO* 3.5 3.8 - - - +
124M GLN* 2.8 28.9 + - - +
125M THR 3.3 24.3 + - - +
126M THR* 3.7 15.9 - - + +
131M LEU* 3.7 23.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il